scanWithPWM: Scan the whole sequence on both strands
In PWMEnrich: PWM enrichment analysis

Description Usage Arguments Details Value Examples

The whole sequence is scanned with a PWM and scores returned beginning at each position. Partial motif matches are not done, thus the last #[length of motif]-1 scores are NA.

scanWithPWM(
  pwm,
  dna,
  pwm.rev = NULL,
  odds.score = FALSE,
  both.strands = FALSE,
  strand.fun = "mean"
)

`pwm`	PWM object
`dna`	a DNAString or other sequence from Biostrings
`pwm.rev`	the reverse complement for a pwm (if it is already pre-computed)
`odds.score`	if to return raw scores in odds (not logodds) space
`both.strands`	if to return results on both strands
`strand.fun`	which function to use to summarise values over two strands (default is "mean")

The function returns either an odds average (*not* log-odds average), maximal score on each strand, or scores on both strands.

The function by default returns the score in log2 following the package Biostrings.

a vector representing scores starting at each position, or a matrix with score in the two strands

if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
   data(MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background")

   ttk = MotifDb.Dmel[["ttk"]]

   # odds average over the two strands expressed as log2-odds
   scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT"))
   
   # log2-odds scores on both strands
   scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT"), both.strands=TRUE)
}